One of my big issues is that while queued up for content, there's not a whole lot we can do without risking missing the queue. So, I'd like to suggest the following changes to make this easier on people.
1: Make the chocobo not count as a party member. Honestly, there's no reason why it should. Sure, one can argue that you can have a party of 8 with all their chocobos out and that it may be unbalanced, but the only places you can use a chocobo can allow you to simply have two parties there anyway, so this won't allow you to do things you can't normally. In any case, chocobos could function like summons and turrets in terms of party allowances, and like minions (which are already mutually exclusive to chocobos!) not be summonable inside instances.
2: Record our gear set when we queue, and allow us to enter the dungeon while on other classes, automatically changing to that gear set when we enter. We've all been there, out doing FATEs on a lower level job or gathering, when the queue pops... and you have aggro from a monster. You're desperately trying to leash them while the timer counts down, but some helpful adventurer decided to grab it off of you... and now you've got to go halfway across the map before you exit combat. Let's allow us to slay and gather in peace, by changing back to our proper job right as we're warping in.
3: Record our crafting progress when we enter. This goes in tandem with the previous suggestion, a big problem with crafting while queued is starting a synth, getting a few moves in, and the queue popping while you've still got a ways to go, and you have a choice of letting the synth fail (or accepting a NQ which can be just as bad), or losing the queue. Rather, I'd propose that entering a dungeon (or disconnecting) while in the middle of a synth would return you right back where you left off: Same gear equipped, same item being made, same durability, quality, CP, crafting buffs (hasty hand, inner quiet, etc.) and state (good, excellent, poor, normal). It would require a little bit more information being stored on the character, but I don't feel it'd add up to very much, and it would add peace of mind.